Thyroid hormone (TH) signals are transduced by two related thyroid receptors (TRs) that regulate gene expression and are members of the nuclear receptor (NR) superfamily, which also includes receptors for steroids, vitamins and fatty acids and a variety of cholesterol and fatty acids and their metabolites. About 20% of current Pharmaceuticals are ligands that bind to NRs, underlining the importance of the NR family. TH regulates fat mass, cholesterol, heart and other functions; thus developing means to selectively regulate TR actions could lead to useful Pharmaceuticals with selective actions. We have utilized X-ray crystallographic information about the TR ligand-binding (LBD) and DMA-binding (DBD) domains to guide placements of mutations on the TR to analyze the mechanism of TR action. This mutagenesis approach has already allowed us to define LBD surfaces for binding downstream coregulators that mediate changes in gene expression, arid for forming TR-TR dimers and heterodimers with the retinoid X-receptor (RXR). The results also identified sites that might be targets for novel Pharmaceuticals. In the proposed studies we use our large bank of mutations and additional proposed mutations to determine: how receptors discriminate between various corepressors; the molecular basis of a novel mode of binding of TR to a coactivator (PGC-1); how the TR and RXR adapt to recognize diverse orientations of their DMA binding sites; mechanisms whereby TH regulates receptor binding to DMA; the role of salt bridges that influence several different TR functions in the unliganded vs. the liganded modes; and how a novel ligand exhibits selectivity for binding a particular TR isoform by inserting a side group between structures outside the ligand-binding cavity. These studies should provide substantial insight into TR function that is relevant for understanding TR action, mechanism of action of other NRs, regulation of gene expression and pharmaceutical design.